Diff of the two buildlogs: -- --- b1/build.log 2023-04-15 04:56:30.690942465 +0000 +++ b2/build.log 2023-04-15 04:57:50.647389146 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 23:17:56 -12 2024 -I: pbuilder-time-stamp: 1715944676 +I: Current time: Sat Apr 15 18:56:34 +14 2023 +I: pbuilder-time-stamp: 1681534594 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +gpgv: Signature made Fri Feb 19 21:13:34 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -31,11 +31,20 @@ dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/26320/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' @@ -45,38 +54,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' - PPID='26320' + PPID='20840' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GqWouEf0/pbuilderrc_Egnn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GqWouEf0/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GqWouEf0/pbuilderrc_bh7q --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GqWouEf0/b2 --logfile b2/build.log --extrapackages usrmerge wham-align_0.1.5-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink11-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 15 05:13 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/26320/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 15 02:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +151,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 1s (13.0 MB/s) +Fetched 18.3 MB in 0s (38.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -276,8 +285,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -361,13 +379,6 @@ pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ -In file included from hitset.h:31, - from hash.h:29, - from hash.cpp:27: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -388,6 +399,45 @@ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] + 685 | int a; + | ^ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from aligner.cpp:25: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -417,23 +467,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~ -pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] - 685 | int a; - | ^ -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from aligner.cpp:25: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; @@ -444,20 +477,13 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': -pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~ -pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ -pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': -pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); - | ~~~~~~~^~~~~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from hash.cpp:27: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); @@ -466,10 +492,23 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': -hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] - 86 | int size; - | ^~~~ +edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] + 61 | int i; + | ^ +edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] + 181 | char tmp_trace = traceback[i][j]; + | ^~~~~~~~~ +edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] + 178 | int kk = 0; + | ^~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -503,10 +542,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; @@ -529,23 +564,6 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] - 61 | int i; - | ^ -edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] - 181 | char tmp_trace = traceback[i][j]; - | ^~~~~~~~~ -edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] - 178 | int kk = 0; - | ^~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:422:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 422 | forward_word = ~((~code) | (-1LL << forward_offset)); @@ -573,8 +591,6 @@ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp -g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -583,14 +599,6 @@ pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from sequence.cpp:30: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -634,14 +642,28 @@ pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from sequence.cpp:30: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; @@ -677,10 +699,6 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); @@ -689,61 +707,10 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -hash.cpp: In member function 'int HashTable::preProcessEnd()': -hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] - 236 | if (h >= nHistogram) - | ~~^~~~~~~~~~~~~ -hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 285 | if (useEmbedTables() && tmp > embedShreshold) { - | ~~~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::setScanThreshold(double)': -hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 343 | for (int i = 0; i < nHistogram - 1; i++) { - | ~~^~~~~~~~~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': -hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] - 460 | overflowPool[curOverflowEntry] = -hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] - 411 | uint32 seqOffset; - | ^~~~~~~~~ -hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] - 413 | uint32 counter = 0; - | ^~~~~~~ -hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 414 | int64 * seqVector; - | ^~~~~~~~~ -hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] - 416 | int64 * target = &tspace[8]; - | ^~~~~~ -hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] - 417 | bool isBloomFilter; - | ^~~~~~~~~~~~~ -hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] - 418 | uint32 * bloomFilter; - | ^~~~~~~~~~~ -hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] - 419 | uint32 bloomFilterNum; - | ^~~~~~~~~~~~~~ -hash.cpp: In member function 'int HashTable::buildEmbedTable()': -hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] - 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], - | ^~~~ -hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] - 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], - | ^~~~~ -hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~ -hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~~~~~ -hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] - 472 | uint32 seqOffset, entryOffset, startOffset; - | ^~~~~~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); @@ -755,20 +722,6 @@ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ -sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': -sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] - 97 | char * str; - | ^~~ -hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': -hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] - 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; - | ^~~~~~~~~ -hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = @@ -793,14 +746,6 @@ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 238 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': -hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] - 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; - | ^~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; @@ -817,6 +762,14 @@ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ +sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': +sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] + 97 | char * str; + | ^~~ +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 238 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ @@ -826,37 +779,18 @@ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ -hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 410 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 429 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': -hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] - 746 | int num; - | ^~~ sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~ sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~~~~~ -hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] - 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~ -hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~~~~~ sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < numFile; i++) { @@ -885,6 +819,125 @@ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::save(char*)': +sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 738 | if (ret != size) { + | ~~~~^~~~~~~ +sequence.cpp: In member function 'int CompactSequence::load(char*)': +sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 804 | if (ret != size) { + | ~~~~^~~~~~~ +main.cpp: In function 'int getArguVal(char*)': +main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 159 | else if (*c = 'g' || *c == 'G') + | ~~~^~~~~~~~~~~~~~~~~~ +main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': +main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp: In function 'int main(int, char**)': +main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] + 523 | int numKeys; + | ^~~~~~~ +main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] + 526 | int nSeq = 1; + | ^~~~ +main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] + 532 | CompactSequence * sequence; + | ^~~~~~~~ +main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] + 534 | pthread_t * threadpool; + | ^~~~~~~~~~ +main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] + 536 | int * threadid; + | ^~~~~~~~ +hash.cpp: In member function 'int HashTable::preProcessEnd()': +hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] + 236 | if (h >= nHistogram) + | ~~^~~~~~~~~~~~~ +hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 285 | if (useEmbedTables() && tmp > embedShreshold) { + | ~~~~^~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::setScanThreshold(double)': +hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 343 | for (int i = 0; i < nHistogram - 1; i++) { + | ~~^~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': +hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] + 460 | overflowPool[curOverflowEntry] = +hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] + 411 | uint32 seqOffset; + | ^~~~~~~~~ +hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] + 413 | uint32 counter = 0; + | ^~~~~~~ +hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 414 | int64 * seqVector; + | ^~~~~~~~~ +hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] + 416 | int64 * target = &tspace[8]; + | ^~~~~~ +hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] + 417 | bool isBloomFilter; + | ^~~~~~~~~~~~~ +hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] + 418 | uint32 * bloomFilter; + | ^~~~~~~~~~~ +hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] + 419 | uint32 bloomFilterNum; + | ^~~~~~~~~~~~~~ +hash.cpp: In member function 'int HashTable::buildEmbedTable()': +hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] + 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], + | ^~~~ +hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] + 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], + | ^~~~~ +hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~ +hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~~~~~ +hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] + 472 | uint32 seqOffset, entryOffset, startOffset; + | ^~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': +hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] + 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; + | ^~~~~~~~~ +hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': +hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] + 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; + | ^~~~~~~~~ +hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': +hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] + 746 | int num; + | ^~~ +hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] + 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~ +hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -898,10 +951,6 @@ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::save(char*)': -sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 738 | if (ret != size) { - | ~~~~^~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; @@ -921,10 +970,13 @@ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ -sequence.cpp: In member function 'int CompactSequence::load(char*)': -sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 804 | if (ret != size) { - | ~~~~^~~~~~~ +aligner.cpp: In member function 'int Aligner::initLookupArray()': +aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 365 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ +aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 371 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) @@ -943,27 +995,13 @@ hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; | ^~~~ -hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1321 | uint32 entryOffset, seqOffset, offset; - | ^~~~~~ -hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': -hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1673 | uint32 entryOffset, seqOffset, offset; - | ^~~~~~ -hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] - 1690 | restart: if (buckets[bucketId] == HASH_EMPTY - | ^~~~~~~ -aligner.cpp: In member function 'int Aligner::initLookupArray()': -aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 365 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ -aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 371 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ +hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1321 | uint32 entryOffset, seqOffset, offset; + | ^~~~~~ aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 712 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ @@ -981,6 +1019,13 @@ aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': +hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1673 | uint32 entryOffset, seqOffset, offset; + | ^~~~~~ +hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] + 1690 | restart: if (buckets[bucketId] == HASH_EMPTY + | ^~~~~~~ aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1036,6 +1081,7 @@ aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] 1039 | int nHit = 0; | ^~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1119 | uint32 offset; @@ -1085,6 +1131,12 @@ aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1685 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ +In file included from hitset.h:31, + from hitset.cpp:1: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1754 | delete writer; | ^~~~~~~~~~~~~ @@ -1117,24 +1169,6 @@ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ -g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp -main.cpp: In function 'int getArguVal(char*)': -main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 159 | else if (*c = 'g' || *c == 'G') - | ~~~^~~~~~~~~~~~~~~~~~ -In file included from hitset.h:31, - from hitset.cpp:1: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': -main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] - 350 | int i, j, ret; - | ^ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -1182,22 +1216,6 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -main.cpp: In function 'int main(int, char**)': -main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] - 523 | int numKeys; - | ^~~~~~~ -main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] - 526 | int nSeq = 1; - | ^~~~ -main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] - 532 | CompactSequence * sequence; - | ^~~~~~~~ -main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] - 534 | pthread_t * threadpool; - | ^~~~~~~~~~ -main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] - 536 | int * threadid; - | ^~~~~~~~ hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; @@ -1207,6 +1225,19 @@ edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ +In file included from pair.h:26: +rdtsc.h: In function 'long long unsigned int curtick()': +rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] + 32 | return tick; + | ^~~~ +rdtsc.h:20:22: note: 'tick' was declared here + 20 | unsigned long long tick; + | ^~~~ +In file included from main.cpp:38: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; @@ -1236,14 +1267,14 @@ | | | | int* unsigned int* | %d -hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] - 1049 | } - | ^ model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ +hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': +hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] + 1049 | } + | ^ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] @@ -1257,19 +1288,6 @@ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ -In file included from pair.h:26: -rdtsc.h: In function 'long long unsigned int curtick()': -rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] - 32 | return tick; - | ^~~~ -rdtsc.h:20:22: note: 'tick' was declared here - 20 | unsigned long long tick; - | ^~~~ -In file included from main.cpp:38: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp In file included from hitset.h:31, from writer.h:26, @@ -1328,6 +1346,25 @@ writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; +main.cpp: In function 'void mergeFiles(std::string)': +main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 269 | sprintf(buf, ".t%d ", i); + | ^~ +main.cpp:269:18: note: directive argument in the range [0, 2147483646] + 269 | sprintf(buf, ".t%d ", i); + | ^~~~~~~ +main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 + 269 | sprintf(buf, ".t%d ", i); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 276 | sprintf(buf, ".t%d", i); + | ^~ +main.cpp:276:18: note: directive argument in the range [0, 2147483646] + 276 | sprintf(buf, ".t%d", i); + | ^~~~~~ +main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 + 276 | sprintf(buf, ".t%d", i); + | ~~~~~~~^~~~~~~~~~~~~~~~ writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~ @@ -1384,25 +1421,6 @@ sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; | ^~~~~~~~~~~~~~ -main.cpp: In function 'void mergeFiles(std::string)': -main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 269 | sprintf(buf, ".t%d ", i); - | ^~ -main.cpp:269:18: note: directive argument in the range [0, 2147483646] - 269 | sprintf(buf, ".t%d ", i); - | ^~~~~~~ -main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 - 269 | sprintf(buf, ".t%d ", i); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 276 | sprintf(buf, ".t%d", i); - | ^~ -main.cpp:276:18: note: directive argument in the range [0, 2147483646] - 276 | sprintf(buf, ".t%d", i); - | ^~~~~~ -main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 - 276 | sprintf(buf, ".t%d", i); - | ~~~~~~~^~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -1411,6 +1429,15 @@ pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ +In member function 'void HashTable::setLookupInfo(int, int*)', + inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: +hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] + 353 | widthKeySpan = keySpan; + | ~~~~~~~~~~~~~^~~~~~~~~ +aligner.cpp: In member function 'int Aligner::initLookupArray()': +aligner.cpp:360:7: note: 'keySpan' was declared here + 360 | int keySpan; + | ^~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -1458,10 +1485,6 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': sequence.cpp:674:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 674 | forward_word = ~((~code) | (-1LL << forward_offset)); @@ -1469,15 +1492,10 @@ sequence.cpp:630:23: note: 'code' was declared here 630 | int64 forward_word, code; | ^~~~ -In member function 'void HashTable::setLookupInfo(int, int*)', - inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: -hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] - 353 | widthKeySpan = keySpan; - | ~~~~~~~~~~~~~^~~~~~~~~ -aligner.cpp: In member function 'int Aligner::initLookupArray()': -aligner.cpp:360:7: note: 'keySpan' was declared here - 360 | int keySpan; - | ^~~~~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ builder.cpp: In function 'int getArguVal(char*)': builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 115 | else if (*c = 'g' || *c == 'G') @@ -1505,7 +1523,7 @@ g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/wham-align-0.1.5' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-cOY8sa6R + rm -fr -- /tmp/dh-xdg-rundir-8K8NJI9S create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1542,10 +1560,10 @@ install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 - mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 - chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 + mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 + chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 dh_perl dh_link dh_strip_nondeterminism @@ -1620,12 +1638,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20840/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/26320 and its subdirectories -I: Current time: Thu May 16 23:19:29 -12 2024 -I: pbuilder-time-stamp: 1715944769 +I: removing directory /srv/workspace/pbuilder/20840 and its subdirectories +I: Current time: Sat Apr 15 18:57:49 +14 2023 +I: pbuilder-time-stamp: 1681534669